Variant report

Variant	rs1317243
Chromosome Location	chr3:112053246-112053247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112052345..112054034-chr3:112155349..112157049,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10511311	0.81[CEU][hapmap]
rs12106673	0.96[CEU][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap];0.96[EUR][1000 genomes]
rs12106967	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13069751	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13069935	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13070091	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13090468	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs13092081	0.90[EUR][1000 genomes]
rs13095299	0.88[EUR][1000 genomes]
rs13098589	0.81[CEU][hapmap]
rs13100916	0.88[EUR][1000 genomes]
rs1879513	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1879514	0.90[ASN][1000 genomes]
rs2272022	0.81[CEU][hapmap]
rs2399412	0.90[EUR][1000 genomes]
rs2399416	0.81[CEU][hapmap]
rs2895395	0.81[CHD][hapmap]
rs4355254	0.81[CHD][hapmap]
rs4682101	0.87[ASN][1000 genomes]
rs4682398	0.90[EUR][1000 genomes]
rs4682399	0.92[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs62264124	0.85[ASN][1000 genomes]
rs6438064	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6438065	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6762106	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6773206	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6780745	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6787547	0.90[ASN][1000 genomes]
rs6798354	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6798486	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6805117	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6805142	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6808365	0.93[ASN][1000 genomes]
rs7639471	0.87[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs7639794	0.82[CHB][hapmap]
rs7647411	0.81[CEU][hapmap]
rs8179893	0.90[EUR][1000 genomes]
rs8179913	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9755930	0.92[ASN][1000 genomes]
rs9814721	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9823309	0.93[ASN][1000 genomes]
rs9834347	0.87[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs9852176	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9856838	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9876973	0.87[ASN][1000 genomes]
rs9990215	0.95[CHB][hapmap]
rs9990216	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs9990220	0.91[CHB][hapmap];0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1317243	CD200	cis	parietal	SCAN
rs1317243	CD200	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112050600-112054200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr3:112050800-112054200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr3:112051000-112053600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr3:112051000-112053800	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr3:112051000-112054000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr3:112051000-112054200	Active TSS	Placenta	Placenta
7	chr3:112051400-112053400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:112051400-112053600	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr3:112051400-112053600	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr3:112051400-112053600	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr3:112051400-112054200	Active TSS	Fetal Brain Female	brain
12	chr3:112051400-112054200	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr3:112051400-112054400	Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr3:112051400-112054400	Active TSS	GM12878-XiMat	blood
15	chr3:112051400-112054600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:112051600-112053400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:112051600-112053600	Active TSS	H1 Cell Line	embryonic stem cell
18	chr3:112051600-112053600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:112051600-112053600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:112051600-112053600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:112051600-112053600	Active TSS	Brain Substantia Nigra	brain
22	chr3:112051600-112053600	ZNF genes & repeats	Fetal Brain Male	brain
23	chr3:112051600-112053600	Active TSS	Fetal Thymus	thymus
24	chr3:112051600-112053600	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr3:112051600-112053800	Active TSS	H9 Cell Line	embryonic stem cell
26	chr3:112051600-112053800	Active TSS	Fetal Intestine Small	intestine
27	chr3:112051600-112054000	Active TSS	Aorta	Aorta
28	chr3:112051600-112054000	Active TSS	Fetal Kidney	kidney
29	chr3:112051600-112054000	Active TSS	Fetal Lung	lung
30	chr3:112051600-112054000	Active TSS	Ovary	ovary
31	chr3:112051600-112054200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:112051600-112054200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:112051600-112054200	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr3:112051600-112054200	Active TSS	Thymus	Thymus
35	chr3:112051600-112054400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:112051600-112054400	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr3:112051600-112054400	Active TSS	Brain Angular Gyrus	brain
38	chr3:112051600-112054400	Active TSS	Brain Hippocampus Middle	brain
39	chr3:112051600-112054400	Active TSS	Rectal Smooth Muscle	rectum
40	chr3:112051600-112054800	Active TSS	Brain Cingulate Gyrus	brain
41	chr3:112051800-112053600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr3:112051800-112053600	Active TSS	Colon Smooth Muscle	Colon
43	chr3:112051800-112053800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:112051800-112053800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:112051800-112053800	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr3:112051800-112055400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:112052000-112053600	Active TSS	Primary B cells from peripheral blood	blood
48	chr3:112052000-112053800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:112052200-112053600	Active TSS	Stomach Smooth Muscle	stomach
50	chr3:112052200-112053800	Active TSS	Duodenum Mucosa	Duodenum

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